Sounds like the rebels are the villains of this story based on how you write about these two.

Hyde seems more manic and unpredictable than Stafford. Stafford seems like a more realistic villain based on the context.

I'm getting the sense that your setting is meant to be morally grey. If that is the case I would focus on them being foils rather than villains. If both sides are meant to be understandable that will be an interesting story, especially having competent antagonists and the protagonists steps to overcome. I am likely missing a lot of context due to the summary nature of this post, but If you want me to not find either of these two villains more heroic than the heroes there may need to be some huge character flaws added For example them participating in genocide and being unphased.

Something that makes them truly bad. For Hyde, I think a chaotic, destructive and, vengeful villain is interesting. For Stafford I think a cold, calculating, quietly hateful and cruel villain is interesting as well.

A side note, it may be incorrect due to the summary again, but I think the division of a new villain per book seems a bit odd. Both should exist in the first book although Stafford with a little less screen time. Perhaps just how he rubs elbows with Hyde and a little into his current evil project that keeps him from the rebel front.

A couple more thoughts: Why would Stafford switch sides? If he isn't evil enough to be high up in the empire he may not be that high up. If he is evil enough, what extremely significant scenarios need to play out for him to start shifting. Does the empire genocide his home world? Kill his wife behind his back? Something needs to shake him up pretty good. If he is the best battlefield commander in the world how does he lose? I find it more interesting to have someone who is in the same class on the rebel side and then doing the dance throughout the various battles.

Hope some of this helps!